The all north-west clash on Saturday, 11 May sees the 42-year-old take charge of the showpiece for the first time.
Marriner has refereed at Wembley twice before, in the 2010 Community Shield between Manchester United and Chelsea, and the Championship play-off final contested by Cardiff and Blackpool earlier that year.
He was the fourth official for the 2011 FA Cup Final, which saw Manchester City beat Stoke City 1-0.
"It's a great honour to be asked to referee the 2013 FA Cup final, especially as it coincides with the 150th anniversary of the Football Association," Marriner said.
"To be involved in the FA Cup final is ultimately every schoolboy's dream and, as an occasion, they don't come much bigger.
"I'll approach the final as I would any other fixture but obviously the whole event is on a completely different scale as it is the biggest club game in world football."
Marriner's team of match officials for the final comprises assistant referees Stephen Child and Simon Long and fourth official Anthony Taylor.